| | By Darleen Hartley @ Saturday, March 21, 2009 8:15 AM
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| | A university in Sweden is gearing up to provide researchers with a powerful system for large scale computing and data storage. Grants are helping Uppsala University's UPPMAX (Uppsala Multidisciplinary Center for Advanced Computational Science) expand its operations.
 Sequencing technology gives researchers a chance to understand the impact of the genome on the genesis of common diseases. Uppsala University will provide the computers to handle the volume of data necessary to do the analysis.
This technology makes it possible to map all the bacteria in a person's mouth, to try to discover why one person develops malaria while another does not. They’ll try to find how the malaria parasite adapts in order to avoid the body’s immune defenses.
The system could also help to catalogue all the DNA modifications in a cancer cell. Regions in our genes increase the risk of various common diseases such as cancer and diabetes. These regions were identified using so-called SNP (single nucleotide polymorphismschips), but it has been difficult to identify the actual mutations that cause disease.
Kerstin Lindblad-Toh, professor of comparative genomics, says, 'The new sequencing methods supported by this funding offer tremendous potential for finding many of these mutations. Knowledge about the mutations and disease mechanisms will enable development of better, more targeted drugs.'
Hugh amounts of data are accumulated in these studies and it takes many terabytes of data storage and primary memory to manage and analyze these data. The university was recently granted $1.5 million from the Knut and Alice Wallenberg Foundation (KAW) to build a computing system to enhance their existing sequencing platform’s ability. Their three new technology sequencing machines make Uppsala University the largest Nordic player in this field.
Large-scale computations and large-scale storage, processing, and analysis of data play an ever greater role in many scientific fields. The Swedish National Infrastructure for Computing (SNIC) announced, together with KAW, that funding was available. KAW contributed investment capital, and SNIC operational and user support.
Two of eight applications submitted were granted. Both projects involve Uppsala researchers. One is for research on new energy materials, and the other is the visionary genome-sequencing research.
The new computer system for DNA sequencing will be located at UPPMAX and will be run by the Center's systems experts. Since its establishment in 2003, UPPMAX has provided local and national researchers with computational power from a number of computer clusters. A 2008 allocation from SNIC is earmarked for a new cluster of some 2000 computing cores, and is under procurement. The latest grant will add another cluster.
A dozen leading researchers collaborated on the application to satisfy the need to deal with the enormous quantities of data from modern sequencing technology. The researchers who all work with different biological problem complexes submitted a joint application.
“Our activities are expanding to include extensive data storage, some 500 terabytes, says Ingela Nyström, UPPMAX director. “Some data will have to be stored up to ten years, which places special demands on the technology.' X
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